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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH SYNTHETIC OPERATOR 9C
 
Authors :  D. Watkins, G. B. Koudelka, L. D. Williams
Date :  18 Sep 09  (Deposition) - 19 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Dna-Binding, Repressor, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Watkins, S. Mohan, G. B. Koudelka, L. D. Williams
Sequence Recognition Of Dna By Protein-Induced Conformational Transitions
J. Mol. Biol. V. 396 1145 2010
PubMed-ID: 20053356  |  Reference-DOI: 10.1016/J.JMB.2009.12.050

(-) Compounds

Molecule 1 - 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP *TP*A)-3'
    Chains: A
    Engineered: YES
    Other Details: SYNTHETIC DNA OPERATOR 9C
    Other Details - Source: SYNTHETIC DNA OPERATOR 9C
    Synthetic: YES
 
Molecule 2 - 5'-D(*TP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP *TP*G)-3'
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC DNA OPERATOR 9C
    Other Details - Source: SYNTHETIC DNA OPERATOR 9C
    Synthetic: YES
 
Molecule 3 - REPRESSOR PROTEIN C2
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Strain: XA90
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C2
    Organism Common: BACTERIOPHAGE P22
    Organism Scientific: ENTEROBACTERIA PHAGE P22
    Organism Taxid: 10754

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3JXB)

(-) Sites  (0, 0)

(no "Site" information available for 3JXB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JXB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JXB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JXB)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.RPC2_BPP2210-64
 		  2C:10-64
D:10-64

(-) Exons   (0, 0)

(no "Exon" information available for 3JXB)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:DNA  Length:20
                                                   
                  3jxb A  1 CATTTAAGACGTCTTAAATA 20
                                    10        20


Chain B from PDB  Type:DNA  Length:20
                                                   
                  3jxb B 21 TATTTAAGACGTCTTAAATG 40
                                    30        40


Chain C from PDB  Type:PROTEIN  Length:67
 aligned with RPC2_BPP22 | P69202 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:67
                                    11        21        31        41        51        61       
            RPC2_BPP22    2 NTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
               SCOP domains d3jxbc_ C: P22 C2 repressor, DNA-binding domain                     SCOP domains
               CATH domains 3jxbC00 C:2-68 lambda repressor-like DNA-binding domains            CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------HTH_CROC1  PDB: C:10-64 UniProt: 10-64                 ---- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3jxb C  2 NTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
                                    11        21        31        41        51        61       


Chain D from PDB  Type:PROTEIN  Length:65
 aligned with RPC2_BPP22 | P69202 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:65
                                    13        23        33        43        53        63     
            RPC2_BPP22    4 QLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
               SCOP domains d3jxbd_ D: P22 C2 repressor, DNA-binding domain                   SCOP domains
               CATH domains 3jxbD00 D:4-68 lambda repressor-like DNA-binding domains          CATH domains
           Pfam domains (1) ------HTH_3-3jxbD01 D:10-64                                  ---- Pfam domains (1)
           Pfam domains (2) ------HTH_3-3jxbD02 D:10-64                                  ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HTH_CROC1  PDB: D:10-64 UniProt: 10-64                 ---- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3jxb D  4 QLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
                                    13        23        33        43        53        63
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,D   (RPC2_BPP22 | P69202)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RPC2_BPP22 | P69202: 1adr 1qar 2r1j 3jxc 3jxd

(-) Related Entries Specified in the PDB File

3jxc CRYSTAL STRUCTURE OF P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH SYNTHETIC OPERATOR 9T IN THE PRESENCE OF TL+
3jxd CRYSTAL STRUCTURE OF P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH SYNTHETIC OPERATOR 9C IN PRESENCE OF RB+